Vienna package for RNA structure analysis

The Vienna RNA packages consists of a few stand alone programs and a library that you can link your own programs with. The package allows you to

There is also a set of programs for analysing sequence and distance data using split decomposition, statistical geometry, and cluster methods.

This version contains a Perl 5 module that allows to access all functions of the library from perl scripts, see the Perl subdirectory. In addition a new program for calculating all suboptimal structures within a given energy range can be found in the Subopt directory.

The following executables are provided:
AnalyseDists Analyse a distance matrix
AnalyseSeqs Analyse a set of sequences of common length
RNAdistance Calculate distances of RNA secondary structures
RNAeval Calculate energy of RNA sequences on given secondary structure
RNAfold Calculate secondary structures of RNAs
RNAheat Calculate specific heat of RNAs
RNAinverse Find RNA sequences with given secondary structure
RNApdist Calculate distances of thermodynamic RNA secondary structures ensembles
RNAplot Draw RNA Secondary Structures
RNAsubopt Calculate suboptimal secondary structures of RNAs

All executables read from stdin and write to stdout and use command line switches rather than menus to be easily usable in pipes.

We have included a patched version of D.G. Gilbert's readseq program for those who often process sequence files from databanks.

Example: 

readseq -f=19 -a file_in_some_strange_format | RNAfold | RNAdistance -Xm -Dh | AnalyseDists -Xn

will convert all sequences in the file, fold them, calculate all pair distances between the resulting secondary structures and construct a phylogentic tree of the structures using the neighbour joining algorithm.

The code very rarely uses static arrays, and all programs should work for sequences up to a length of 32700 (if you have huge amounts of memory that is).

We need your feedback! Send your comments, suggestions, and questions to rna@tbi.univie.ac.at